Integration of Combine PEP Node

tests/integrationtests/wrappers/test_combine_pep.py

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+"""Tests for the CombinePEP:1.0.0 unode."""
+
+import csv
+
+from pathlib import Path
+
+import pytest
+
+import urgap
+
+
+def test_wrapper_combine_pep_1_0_0_two_engines(tmp_dir: Path) -> None:
+    """Test that CombinePEP correctly combines PEPs across Casanovo and X!Tandem."""
+    ufiles = urgap.UFileList(
+        [
+            urgap.UFile(
+                uri=f"file://{urgap._test_folder}/data?uftype="
+                f"{urgap.uftypes.proteomics.validator.PERCOLATOR_CSV}#percolator_files/percolator_casanovo.csv",
+            ),
+            urgap.UFile(
+                uri=f"file://{urgap._test_folder}/data?uftype="
+                f"{urgap.uftypes.proteomics.validator.PERCOLATOR_CSV}#percolator_files/percolator_xtandem.csv",
+            ),
+        ],
+    )
+
+    urun_dict = urgap.URunDict(
+        {
+            "parameters": {
+                "CombinePEP:1.0.0": {
+                    "psm_defining_colnames": [
+                        "spectrum_id", "sequence", "modifications", "charge",
+                    ],
+                    "window_size": 100,
+                },
+            },
+            "unode_parameters": {
+                "storage_base_uri": f"file://{tmp_dir}",
+            },
+        },
+    )
+    node = urgap.init_unode("CombinePEP:1.0.0")
+    output_files = node.run(
+        ufiles,
+        urun_dict,
+    )
+    assert output_files[0].path.exists() is True
+
+    with output_files[0].path.open(newline="") as test_file:
+        rows = list(csv.DictReader(test_file))
+
+    assert "Bayes PEP" in rows[0]
+    assert "combined PEP" in rows[0]
+    assert "combined PEP engines" in rows[0]
+
+    # 2971 casanovo-only + 2977 xtandem-only + 43 shared PSMs written once per
+    # engine (86 rows) = 6034 data rows
+    assert len(rows) == 6034
+
+    # PSM (spectrum_id=7498, sequence=DGTITETDGSTR, modifications="", charge=2)
+    # is one of the 43 PSMs shared by both engines. Its two output rows should
+    # both carry the same Bayes PEP, computed from casanovo PEP 0.000193267 and
+    # xtandem PEP 0.180512.
+    shared_psm_rows = [
+        row for row in rows
+        if row["spectrum_id"] == "7498" and row["sequence"] == "DGTITETDGSTR"
+    ]
+    assert len(shared_psm_rows) == 2
+
+    for row in shared_psm_rows:
+        assert row["combined PEP engines"] == "casanovo_5_0;xtandem_alanine"
+        assert float(row["Bayes PEP"]) == pytest.approx(4.2578e-05, rel=1e-3)
+
+
+def test_wrapper_combine_pep_1_0_0_single_engine(tmp_dir: Path) -> None:
+    """Test that CombinePEP runs correctly with only one engine's PSMs."""
+    ufiles = urgap.UFileList(
+        [
+            urgap.UFile(
+                uri=f"file://{urgap._test_folder}/data?uftype="
+                f"{urgap.uftypes.proteomics.validator.PERCOLATOR_CSV}#percolator_files/percolator_xtandem.csv",
+            ),
+        ],
+    )
+
+    urun_dict = urgap.URunDict(
+        {
+            "parameters": {
+                "CombinePEP:1.0.0": {
+                    "psm_defining_colnames": [
+                        "spectrum_id", "sequence", "modifications", "charge",
+                    ],
+                    "window_size": 100,
+                },
+            },
+            "unode_parameters": {
+                "storage_base_uri": f"file://{tmp_dir}",
+            },
+        },
+    )
+    node = urgap.init_unode("CombinePEP:1.0.0")
+    output_files = node.run(
+        ufiles,
+        urun_dict,
+    )
+    assert output_files[0].path.exists() is True
+
+    with output_files[0].path.open(newline="") as test_file:
+        rows = list(csv.DictReader(test_file))
+
+    # single-engine run: 3020 unique PSM keys (dict-collapsed from 3023 raw rows)
+    assert len(rows) == 3020
+
+    # single-engine test: every row's "combined PEP engines" value should be
+    # exactly the one engine name
+    assert rows[0]["combined PEP engines"] == "xtandem_alanine"

urgap/resources/combine_pep/1_0_0/__init__.py

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+"""Init Combine PEP Resources."""
+
+# Do not modify